Blog Archives
Now that I have a CDS, what do I do with it?
Well, the end game of the CDS is to supply information that can be used to create methods and acquire data.
Here we’ll look at the Acquisition List side of the equation.
Here in the data we retrieved from a CDS or PMD file is stored.
Note that PMD files do not contain all instrument information but this can be added to a CDS and then adjusted.
From here you can select the export SRM data in the Method View tab and an Xml file containing the instrument specific data will be produced.
If you open this file in a text editor such as note pad it will contain the information in the Acquisition List in a format that can be imported into the Instrument Method editor.
If on the Batch View section or the final page of the Acquisition Mode wizard you select Auto-TSRM update this information is passed to the mass spec at the time of acquisition. This allows the user to collect only the data needed to be processed and allows for manual updates in the batch to be automatically loaded to the mass spec at run time. This does not monitor the RT of peaks and automatically update the mass spec controller, but allows for user input to occur in on place versus having to open the instrument editor for a second adjustment.
Compound Data Store or Compound Database – Kinda the same thing….
TF has the concept of bring in a data you know about compounds and storing it for later use.
This we call the Compound Data Store (CDS), but what’s in a name… Its a an XML file that contains information about the compound.
The picture above shows this data in excel. It contains information like the compound name, experiment type, collicion energy, retention time, fragments relationships.
Attached here is a copy of the csv template TEMPLATE.
This information can be edited in excel and uploaded into TF to add to a database or to alter the data base. The changes will be reflected in the TF CDS module.
Once the data is in the CDS, a method developer can utilize it to create processing methods which in turn can be used in syncing acquistion methods in the Master Method.
A blog post to come later this week will highlight the use of the information in the Auto-SRM feature.
A quick note is that the CDS is not automatically turned on at installation.
The user will have to configure the option and restart TF to take advantage of this feature.
Custom Reports Suddenly Stop Working????? Here’s a reason and a Fix!!!!
If you (suddenly) get an error like the following (which may vary depending on OS) when generating custom reports, it is likely caused by a recent security update for MS Office.
Good news is that Microsoft realized this problem and provided a “fix it” tool at http://support.microsoft.com/kb/2703186.
This is what happens based on my investigation if you care:
There is an EXD file created for some VB 6.0 runtime files when you use the controls provided by the runtime files in the Visual Basic designer. Those files are located in %APPDATA%\Microsoft\Forms\ folder (which may vary depending on OS). The problem is that, when security update installs new versions of certain runtime files, the EXD files become invalid and hence this error occurs.
To fix the error, you need to delete the EXD files and they will be re-created as needed. To delete those files, you can either use Microsoft provided “fix it” tool from the link above, or go to the folder directly and delete them.
This link http://technet.microsoft.com/en-us/security/bulletin/ms12-027 gives you some details why the security update is necessary and which software are affected.
Converting From Old to New… Methods, Data and Templates
TraceFinder provides an executable application the top level menu “Go” item, that will allow you to convert all of your old stuff to the latest versions of TraceFinder for use.
This includes all previous versions of TraceFinder and back to the LabForms 2.5.x application.
This allows you to reproduce your data and methods you currently use in the newer platform without having to recreate everything.
It also allows you to browse to any stored TF or LabForms directories to pull in the information even if, it has been archived on a remote disk.
After you have opened the directory the contents for the selected data type will be listed below.
You can select individual files or right click and select all. the simply press the “Start Converting” button in the lower right corner.
If any issues occur the Status column will contain an entry and the log file will record the issues with conversion.
Sample List???…. Do I need a Sample List??? Yes and here’s how to import one
So the basic element of data navigation and collection is a list of samples.
This list will identify the properties of the data collected and tell the system, what to do to and the names of the files collected or to be collected.
So TF has a couple of different ways to do this.
The first and easiest is to make a template of the defined sample grid you want to use. In TraceFinder, the user can define the columns that are displayed in both the data results and sample definition grids.
In Batch View or in the sample page of the Acquisition Mode/Wizard, right click the mouse in the grid and a menu dialog that opens up.
In that dialog , select “Export to CSV”. This will make a copy of the grid and the header lables is a file that can be opened by any editing grid application. The most common is Excel, but you could open in a text editor also.
Simply, open the file and for daily use just input sample information in the template and save as a daily/batch .csv file.
A LIMS system, can create a .csv file in this same format or even use a bar code reader to fill in certain fields even in Excel.
Once the sample input is done save the file as .csv and close the editor.
If the file is still open in Excel, MS Office will not let it be used by another program so TF can’t import it until it’s closed.
Right click in the grid and select “Import Samples”.
The Dialog below opens, then select the appropriate file.
The information contained in the CSV file will be inserted into the grid either at the end of the current data or where the index indicator is if that is the option selected in the drop down list below the browse section.
There is also a xml format that can be created fromat LIMS system that can be used, or if Xcalibur has previously been in use the .sld files can be utilized also. Any sample type that TF does not recognize will be set to the Unknown Sample type.
TraceFinder: Direct Knowledge 